Physical Variables Influencing Near-shore Habitat Use of Juvenile Chinook Salmon in the Sacramento River

Michael  Hellmair    

Physical Variables Influencing Near-shore Habitat Use of Juvenile Chinook Salmon in the Sacramento River

U.S. Army Corps of Engineers

•  Evaluate habitat use of focal fish species at various post-2006 levee repair sites

•  Determine if on-site mitigation features are increasing habitat value to approximate “natural banks”

•  Identify which microhabitat features of maximize fish use by focal species

Background & Introduction

Methods: Locations

Sampling occurred at 16 sites, encompassing 3 site categories: –  Naturalized sites (n=4) –  Unmitigated repair sites ( n=3) –  Mitigated repair sites (n=9)

Unmitigated Repair Mitigated Repair

Naturalized

Methods: Sampling

Sampling by boat electrofishing

Methods: Sampling

Measure associated habitat characteristics at each incursion point

Methods: Sampling

Establish point-specific capture record & habitat parameters

Habitat variables: •  Depth / Slope •  Velocity / Gradient •  Substrate •  Temperature difference •  Shade •  Emergent woody

material •  Emergent vegetation

Methods: Variables

Others: •  Event •  Rivermile •  Site/design category

Methods: Habitat Occupancy •  Single-variable logistic regression model to determine if

model fit is significantly improved by any one predictor:

•  Remove non-significant (p> 0.25) predictors from scope for multi-variable model fits

•  Use backward model selection to determine the most likely multivariate model

Pi =eg(x )

(1+ eg(x ) )

Methods: Habitat Occupancy •  Test fit of the selected model using Hosmer-Lemeshow

goodness-of-fit statistic (a high p-value indicates a good fit)

•  Evaluate classification accuracy with unbiased jackknife estimator

•  Determine Cohen’s kappa statistic as a chance-corrected measure of prediction

Results: Habitat Value of Mitigated Repair Sites

•  Fish densities at mitigated repair sites (all designs) were not significantly different from naturalized sites

•  Fish densities at most mitigated repair sites were significantly higher than at non-mitigated sites

Results: Fry Habitat Occupancy

Variables excluded due to non-significance in single model evaluation: •  Shade •  Substrate (at 15 feet) Multivariate model fitting: Final model •  Vegetation density •  Depths close to shore (5 & 10 feet) •  Velocity close to shore (5 & 10 feet) •  Current gradient •  Substrate close to shore (5 & 10 feet) •  Rivermile

Results: Fry Habitat Occupancy

Occupancy probability key factors

Higher probability at points with: •  Submerged vegetation (sparse, OR = 2.07) Lower probability at points with: •  Deep water close to shore (OR = 0.63) •  Faster current close to shore (OR = 0.46)

Hosmer-Lemeshow GOF: p = 0.34 Jackknife : 88% classified correctly Cohen’s kappa: 0.29 (Z = 6.54, p < 0.01)

Results: Juvenile Habitat Occupancy

Variables excluded due to non-significance in single model evaluation: •  Shade •  Depth (at 15 feet) Multivariate model fitting: Final model •  Bank slope •  Density of woody material •  Depths close to shore •  Current gradient •  Temperature difference •  Substrate •  Rivermile

Results: Juvenile Habitat Occupancy

Occupancy probability key factors

Higher probability at points with: •  woody material (sparse OR = 1.78,

medium OR = 2.71) •  warmer ambient temperatures (OR = 1.64) Lower probability at points with: •  Deep water close to shore (> 5ft, OR =

0.06) •  Cooler ambient temperatures (OR = 0.45) Hosmer-Lemeshow GOF: p = 0.46 Jackknife : 81% classified correctly Cohen’s kappa: 0.27 (Z = 5.96, p < 0.01)

Results: Smallmouth Bass

Variables excluded due to non-significance in single model evaluation: •  Vegetation density •  Depth at 10 and 15 feet •  Velocity gradient •  Substrate

Multivariate model fitting: •  Bank slope •  Density of woody material •  Nearshore current velocity •  Rivermile

Higher chance of occupancy at: •  Steep slopes (OR 2.78) •  Density of woody material (OR, Low: 1.93, Medium: 3.06 , High: 11.11) •  Velocity close to shore (Medium, OR 3.31) •  Abundance decreases with distance upstream (OR 0.98)

Resident Rearing vs. Migration

•  Collect drift samples at select sites •  Gastric lavage of juvenile Chinook •  Dissection of mortalities

Key points: •  Majority of individuals had identifiable gastric contents (>95%) •  Often large number of diet items (~200) suggestive of active feeding •  Seasonally high abundance of larval native fishes in drift and diet

–  Larval fishes can constitute > 60% of drift items

•  Typically, copepods and cladocerans constitute > 90% of prey items

Questions?